When a dispenser is activated (by any means) and there is a skull in it, the dispenser does not fire it out as an item entity. It also doesn't equip it to armor stands. It seems as if the dispenser doesn't recognize that the skull is even in it, because it makes the sound and animation that an activated dispenser makes when it is empty. However, comparators can detect it while it is inside.
WAI. MC-48239